I've been using
Total Commander as my main file manager since the 9x days - I use it on nearly every system I run (old PCs down to windows 3.1, Android, Pocket PC, etc). It has a function for connecting two computers
through a parallel port using a direct wired dual-male parallel cable. On the DOS computer, you can run a file server to let a newer computer interact with files on the server side using a program called
LPTDOS which is small enough to be included on a DOS boot disk. This is how I used to do most file transfers to and from older systems - even ancient computers with only floppy. I assume it still works on all Windows environments.
I've never had a problem with any USB floppy drives - most were brand names I didn't recognize. They were all new hardware or barely used old hardware. I also have a floppy drive that runs through PCMCIA, and I hear that you can get a device called backpack that lets you connect a floppy drive through a parallel port.
DOS can handle multiple hard drives, but they need to be partitioned properly for it to work with them - it has a maximum partition size it can work with (Can't remember which size). It deals with larger hard drive sizes by using multiple partitions on the same drive. It can make the partitions itself on a large drive so it can write to it.